Quite a bit of thread necromancy here, but I remembered that your question had never been properly answered. I have actually recently been interested in playing some games based on the Crusades, and so have also been looking for a decent rules set for medieval games. I first looked over Rebellion, as I myself suggested--but was turned off immediately by the use of different types of dice. Hithero and Raukov both suggested using SBG rules for your medieval games; after a lot of searching, I would agree. Google "Age of the Trebuchet." You should find a pdf for a rules set that is adapted from SBG for the Middle Ages! At the beginning I think it even includes hithero as a contributor.
I feel like the Middle Ages should be one of the most popular periods in both video games and wargaming, but its actually quite hard to come by. There's a good amount of companies with very small, not-so-great ranges for the Middle Ages. I think the best recommendations I can make is Perry for early Medieval, eBob for high Medieval, and Perry again for late Medieval. Personally, I am planning on using Age of the Trebuchet to play games set in the later Crusades, with eBob for the Crusaders, and Perry for the Muslims (his Muslim range can quite possibly be used throughout).
If anyone has some suggestions for 28mm plastics in the high Middle Ages, I'd also like to know!
Edit: After all that, I ended up changing my mind; I'm adapting the War of the Ring to the Middle Ages, and switched from 28mm to 1/72 scale models.
I'll periodically post progress in my "Non-LotR showcase" thread.